Query 025326
Match_columns 254
No_of_seqs 116 out of 1125
Neff 9.5
Searched_HMMs 46136
Date Fri Mar 29 04:43:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025326.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025326hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1470 Phosphatidylinositol t 100.0 6.7E-43 1.4E-47 288.3 18.7 201 30-246 45-245 (324)
2 KOG1471 Phosphatidylinositol t 100.0 4.1E-41 8.8E-46 287.9 18.9 214 30-247 41-260 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 1.1E-33 2.3E-38 218.5 10.9 154 84-243 3-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 4.5E-31 9.7E-36 203.7 14.5 150 88-245 9-158 (158)
5 cd00170 SEC14 Sec14p-like lipi 100.0 1.9E-27 4E-32 182.5 12.9 145 90-243 11-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.7 5.6E-17 1.2E-21 123.8 5.0 141 90-246 4-146 (149)
7 PF03765 CRAL_TRIO_N: CRAL/TRI 99.0 8.5E-10 1.8E-14 69.2 5.6 54 4-58 1-55 (55)
8 KOG4406 CDC42 Rho GTPase-activ 98.4 1.3E-06 2.7E-11 74.8 8.9 126 95-236 89-215 (467)
9 PF14555 UBA_4: UBA-like domai 93.9 0.26 5.6E-06 28.7 5.2 24 32-55 13-36 (43)
10 PF00627 UBA: UBA/TS-N domain; 93.5 0.34 7.4E-06 27.1 5.0 25 31-55 13-37 (37)
11 PF02845 CUE: CUE domain; Int 93.3 0.31 6.8E-06 28.2 4.8 27 31-57 14-40 (42)
12 smart00546 CUE Domain that may 86.3 2.5 5.4E-05 24.4 4.6 26 31-56 15-40 (43)
13 PF06972 DUF1296: Protein of u 77.7 11 0.00024 23.5 5.1 27 31-57 18-44 (60)
14 PF08938 HBS1_N: HBS1 N-termin 74.3 1.1 2.3E-05 30.0 0.1 26 33-58 45-70 (79)
15 smart00165 UBA Ubiquitin assoc 73.3 6.9 0.00015 21.5 3.4 25 31-55 12-36 (37)
16 cd00194 UBA Ubiquitin Associat 73.0 7.1 0.00015 21.6 3.4 25 31-55 12-36 (38)
17 KOG1534 Putative transcription 69.5 16 0.00034 29.6 5.6 107 123-235 74-193 (273)
18 TIGR00116 tsf translation elon 56.6 30 0.00064 29.4 5.4 40 2-57 3-42 (290)
19 COG2938 Uncharacterized conser 53.7 17 0.00037 25.1 2.9 43 2-44 44-88 (94)
20 PF03474 DMA: DMRTA motif; In 52.8 29 0.00064 19.7 3.3 24 32-55 15-38 (39)
21 PRK09377 tsf elongation factor 50.3 42 0.00091 28.5 5.3 40 2-57 4-43 (290)
22 PRK12332 tsf elongation factor 48.8 52 0.0011 26.2 5.4 40 2-57 3-42 (198)
23 PF04378 RsmJ: Ribosomal RNA s 47.4 9.9 0.00021 31.3 1.2 30 185-214 205-234 (245)
24 COG2961 ComJ Protein involved 46.8 13 0.00029 30.6 1.8 27 186-212 237-263 (279)
25 PRK10878 hypothetical protein; 46.1 68 0.0015 21.0 4.7 27 32-58 33-59 (72)
26 TIGR02886 spore_II_AA anti-sig 44.1 88 0.0019 21.5 5.6 51 150-204 40-90 (106)
27 PF04838 Baculo_LEF5: Baculovi 44.1 20 0.00043 27.0 2.2 48 170-218 17-68 (159)
28 smart00804 TAP_C C-terminal do 43.1 54 0.0012 20.8 3.8 28 31-58 24-51 (63)
29 CHL00098 tsf elongation factor 41.8 71 0.0015 25.5 5.2 38 4-57 2-39 (200)
30 cd06844 STAS Sulphate Transpor 38.2 1.1E+02 0.0024 20.8 5.3 51 150-204 40-90 (100)
31 PF03641 Lysine_decarbox: Poss 37.3 69 0.0015 23.5 4.3 43 187-231 86-133 (133)
32 PF01740 STAS: STAS domain; I 36.5 47 0.001 23.3 3.2 50 150-203 49-98 (117)
33 PF02954 HTH_8: Bacterial regu 36.2 58 0.0013 18.4 3.0 22 34-55 7-28 (42)
34 PHA02450 hypothetical protein 35.8 15 0.00032 21.5 0.3 12 239-250 12-23 (53)
35 PF03937 Sdh5: Flavinator of s 34.8 61 0.0013 21.2 3.2 23 3-25 33-55 (74)
36 PF03943 TAP_C: TAP C-terminal 34.0 34 0.00073 20.6 1.8 26 31-56 12-37 (51)
37 TIGR00377 ant_ant_sig anti-ant 33.5 1.6E+02 0.0034 20.1 5.7 52 149-204 43-94 (108)
38 COG2994 HlyC ACP:hemolysin acy 32.7 56 0.0012 24.4 3.0 71 94-186 57-128 (148)
39 cd07041 STAS_RsbR_RsbS_like Su 32.1 1.5E+02 0.0033 20.3 5.3 51 150-204 42-92 (109)
40 cd07043 STAS_anti-anti-sigma_f 31.9 1.5E+02 0.0033 19.5 5.7 51 150-204 39-89 (99)
41 PF04548 AIG1: AIG1 family; I 31.8 1.9E+02 0.0041 22.9 6.3 71 149-219 49-122 (212)
42 PF14213 DUF4325: Domain of un 31.6 1.5E+02 0.0032 19.2 5.1 49 150-201 18-68 (74)
43 cd00392 Ribosomal_L13 Ribosoma 31.5 1.1E+02 0.0024 22.0 4.3 38 152-194 2-46 (114)
44 PF13466 STAS_2: STAS domain 30.8 1.5E+02 0.0032 19.0 5.3 51 150-204 27-77 (80)
45 TIGR02364 dha_pts dihydroxyace 30.6 1.3E+02 0.0028 21.9 4.7 50 147-206 59-108 (125)
46 cd07042 STAS_SulP_like_sulfate 29.5 1.6E+02 0.0034 19.9 4.9 50 150-203 42-91 (107)
47 PF13432 TPR_16: Tetratricopep 28.9 1.4E+02 0.003 18.1 5.2 25 36-60 35-59 (65)
48 cd01886 EF-G Elongation factor 28.5 2.6E+02 0.0057 23.3 6.8 35 31-65 209-243 (270)
49 KOG1838 Alpha/beta hydrolase [ 28.4 4.4E+02 0.0095 23.7 9.5 85 97-202 122-214 (409)
50 COG0052 RpsB Ribosomal protein 27.8 51 0.0011 27.2 2.3 65 180-246 31-103 (252)
51 COG1219 ClpX ATP-dependent pro 27.1 34 0.00075 29.6 1.3 22 34-55 144-165 (408)
52 PRK06394 rpl13p 50S ribosomal 25.0 1.4E+02 0.003 22.6 4.0 66 148-222 28-107 (146)
53 PF07862 Nif11: Nitrogen fixat 24.8 1.5E+02 0.0033 17.2 4.5 44 3-50 2-45 (49)
54 TIGR01077 L13_A_E ribosomal pr 24.3 1.1E+02 0.0025 22.9 3.5 68 147-222 23-102 (142)
55 COG0264 Tsf Translation elonga 24.2 2.1E+02 0.0045 24.4 5.3 40 2-57 4-43 (296)
56 PF12452 DUF3685: Protein of u 23.7 3.5E+02 0.0075 21.5 6.2 65 2-66 31-97 (193)
57 PRK12751 cpxP periplasmic stre 23.6 2E+02 0.0044 22.1 4.8 59 2-65 57-115 (162)
58 PF13551 HTH_29: Winged helix- 23.0 2.4E+02 0.0052 19.2 4.9 17 2-18 58-74 (112)
59 KOG3923 D-aspartate oxidase [A 21.8 92 0.002 26.7 2.8 44 148-202 182-225 (342)
60 PF04552 Sigma54_DBD: Sigma-54 20.5 1.8E+02 0.0038 22.3 3.9 28 29-56 119-147 (160)
61 PF13801 Metal_resist: Heavy-m 20.3 3E+02 0.0065 18.9 5.4 62 2-65 42-103 (125)
No 1
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=6.7e-43 Score=288.27 Aligned_cols=201 Identities=26% Similarity=0.381 Sum_probs=175.0
Q ss_pred CCCChHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhCCcchhccCCCCCHHHHHHHhhhhcccccCCCCCCCcEEEEccCC
Q 025326 30 QGNPTDTLVRFLKARDWNVSKAHKMLVDCLRWRIENDIDNILAKPILPAELYRAVRDSQLVGVSGYSKEGLPVIAVGVGL 109 (254)
Q Consensus 30 ~~~~d~~llRfL~a~~~dv~ka~~~l~~~~~wR~~~~~d~~~~~~~~~~~~~~~l~~~~~~~~~g~D~~Grpv~~~~~~~ 109 (254)
..++|++++|||+|+||||++|.+++.+++.||+.+++... +...++..++..+ .++..|+|++||||+|+++..
T Consensus 45 ~~~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~----~~~~Ev~~e~~tG-K~yi~G~D~~gRPVl~~~~~~ 119 (324)
T KOG1470|consen 45 KWCSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEV----IEADEVAAELETG-KAYILGHDKDGRPVLYLRPRP 119 (324)
T ss_pred hcCcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccc----cCHHHHHHHhhcC-cEEEecccCCCCeEEEEecCC
Confidence 34689999999999999999999999999999999987651 2345666666554 477889999999999998887
Q ss_pred CCccchhHHHHHHHHHHHHHHHHhhcchhhhhhhCCccccEEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEE
Q 025326 110 STHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYY 189 (254)
Q Consensus 110 ~~~~~~~~~~~~~~~~~~~E~~~~~~l~~~~~~~~~~~~~~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ 189 (254)
+.....+.+...+..++++|..+ ...+.+.+++++++|++|+|+++.+ ++..+.++.++|+||||||+..+
T Consensus 120 ~~qn~~t~~~~~r~~Vy~mE~Ai--------~~lp~~qe~~~~L~D~~~fs~sN~d-~~~~k~~~~~lq~hYPErLg~a~ 190 (324)
T KOG1470|consen 120 HRQNTKTQKELERLLVYTLENAI--------LFLPPGQEQFVWLFDLTGFSMSNPD-IKFLKELLHILQDHYPERLGKAL 190 (324)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHH--------HhCCCCcceEEEEEecccCcccCCC-cHHHHHHHHHHHHhChHHhhhhh
Confidence 76777788888999998887654 3344567889999999999999887 78999999999999999999999
Q ss_pred EEcCCcchHHHHHHhcccCChhhhcceEEecCCCHhHHhhhCCCCCcccccCCCccc
Q 025326 190 IVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGRDELLKVRQLFQLTFLSAHSCNR 246 (254)
Q Consensus 190 vvN~p~~~~~~~~~vk~~l~~~t~~Ki~~~~~~~~~~L~~~i~~~~LP~~~GG~~~~ 246 (254)
++|+||+|..+|+++||||+|+|++||.|+.+ .+.+.++||+++||..+||+...
T Consensus 191 l~~~P~iF~~~wkiikpflDp~t~~Kv~F~~~--~~~l~~~~d~~~l~s~~GG~~~~ 245 (324)
T KOG1470|consen 191 LVNAPWIFQPFWKIIKPFLDPKTASKVKFVEP--KDDLSEYFDESQLPSLFGGKLLF 245 (324)
T ss_pred hcCChHHHHHHHHHhhhccChhhhceeEEecC--hhHHHhhCCccccchhhCCCccc
Confidence 99999999999999999999999999999874 56699999999999999995543
No 2
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=4.1e-41 Score=287.93 Aligned_cols=214 Identities=34% Similarity=0.484 Sum_probs=189.1
Q ss_pred CCCChHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhCCcchhccCCCCCHHHHHHHhhhhcccccCCCCCCCcEEEEccCC
Q 025326 30 QGNPTDTLVRFLKARDWNVSKAHKMLVDCLRWRIENDIDNILAKPILPAELYRAVRDSQLVGVSGYSKEGLPVIAVGVGL 109 (254)
Q Consensus 30 ~~~~d~~llRfL~a~~~dv~ka~~~l~~~~~wR~~~~~d~~~~~~~~~~~~~~~l~~~~~~~~~g~D~~Grpv~~~~~~~ 109 (254)
...+|..|+|||||++||+++|.+++..++.||+++++|.+..+ ... ...+.+..+...+|.|++|+|+++.+.|.
T Consensus 41 ~~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~-~~~---~~~~~~~~~~~~~~~~~~g~~v~~~~~g~ 116 (317)
T KOG1471|consen 41 KYDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFED-FEE---DDELLKYYPQGLHGVDKEGRPVYIERLGK 116 (317)
T ss_pred CCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhc-ccc---chhhhhhccccccccCCCCCEEEEeccCC
Confidence 35678899999999999999999999999999999999998865 211 12223356678899999999999999998
Q ss_pred CCcc----chhHHHHHHHHHHHHHHHHhhcchhhhhhhCCccccEEEEEeCCCCCccccc--chHHHHHHHHhhhhcCcc
Q 025326 110 STHD----KASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALN--QIKLMTVITTIDDLNYPE 183 (254)
Q Consensus 110 ~~~~----~~~~~~~~~~~~~~~E~~~~~~l~~~~~~~~~~~~~~~~IiD~~g~~~~~~~--~~~~~k~~~~~~~~~yP~ 183 (254)
.+.. .....++.++++.-+|......++.+....+.+++|++.|+|++|++++++. ..+.++.++.++|++||+
T Consensus 117 ~~~~~l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~~~~~~~~~~~~~~~~~q~~yPe 196 (317)
T KOG1471|consen 117 IDPKGLLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSHLLKPAPTLLKKILKILQDNYPE 196 (317)
T ss_pred CCcccceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchhHHHHHHHHHHHHHHHHHHhCHH
Confidence 7654 3577888999999999888777888877777889999999999999999985 356799999999999999
Q ss_pred ccceEEEEcCCcchHHHHHHhcccCChhhhcceEEecCCCHhHHhhhCCCCCcccccCCCcccc
Q 025326 184 KTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGRDELLKVRQLFQLTFLSAHSCNRL 247 (254)
Q Consensus 184 rl~~i~vvN~p~~~~~~~~~vk~~l~~~t~~Ki~~~~~~~~~~L~~~i~~~~LP~~~GG~~~~~ 247 (254)
+++++||||+|++|+++|+++||||+++|++||+++++++.++|.++|++++||.+|||++.+.
T Consensus 197 ~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~~~~~~~L~k~i~~~~LP~~yGG~~~~~ 260 (317)
T KOG1471|consen 197 RLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLHSKDKESLLKYIPPEVLPEEYGGTCGDL 260 (317)
T ss_pred hhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecCCCchhhhhhhCCHhhCccccCCCcccc
Confidence 9999999999999999999999999999999999767778999999999999999999999986
No 3
>PF00650 CRAL_TRIO: CRAL/TRIO domain; InterPro: IPR001251 This entry defines the C-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1OLM_E 1O6U_E 3Q8G_A 3B7Q_B 3B7Z_A ....
Probab=100.00 E-value=1.1e-33 Score=218.54 Aligned_cols=154 Identities=27% Similarity=0.426 Sum_probs=125.4
Q ss_pred HhhhhcccccCCCCCCCcEEEEccCCCCccchhHHHHHHHHHHHHHHHHhhcchhhhhhhCCccccEEEEEeCCCCCccc
Q 025326 84 VRDSQLVGVSGYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSA 163 (254)
Q Consensus 84 l~~~~~~~~~g~D~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~l~~~~~~~~~~~~~~~~IiD~~g~~~~~ 163 (254)
+.++++.+++|+|++||||++++++.+++...+.++++++.++++|..++.. +. +.+.+|+++|+|++|+++++
T Consensus 3 ~~~~~~~~~~g~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~-~~-----~~~~~~~~~iiD~~g~~~~~ 76 (159)
T PF00650_consen 3 ILKSGPFYLHGRDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRM-PE-----GGQVEGIVVIIDLSGFSLSN 76 (159)
T ss_dssp HHTTSCEEEEEE-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTH-HH-----TSHHH-EEEEEE-TT--HHH
T ss_pred HHCCeeEEECCCCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhh-cc-----cccceeEEEEEeCCCceEec
Confidence 4567788999999999999999999998887788899999999999876421 11 35678999999999999998
Q ss_pred ccc--hHHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHHhcccCChhhhcceEEecCCCH-hHHhhhCCCCCccccc
Q 025326 164 LNQ--IKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGR-DELLKVRQLFQLTFLS 240 (254)
Q Consensus 164 ~~~--~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~vk~~l~~~t~~Ki~~~~~~~~-~~L~~~i~~~~LP~~~ 240 (254)
++. .+.++.+++++|++||+|++++|++|+|++++.+|+++++|++++|++||+++++.+. ++|.+++|+++||++|
T Consensus 77 ~~~~~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP~~~ 156 (159)
T PF00650_consen 77 FDWWPISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLPVEY 156 (159)
T ss_dssp HHCHHHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSBGGG
T ss_pred cccchhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCchhc
Confidence 863 5789999999999999999999999999999999999999999999999999965433 7999999999999999
Q ss_pred CCC
Q 025326 241 AHS 243 (254)
Q Consensus 241 GG~ 243 (254)
||+
T Consensus 157 GG~ 159 (159)
T PF00650_consen 157 GGT 159 (159)
T ss_dssp TSS
T ss_pred CCC
Confidence 997
No 4
>smart00516 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.97 E-value=4.5e-31 Score=203.66 Aligned_cols=150 Identities=25% Similarity=0.408 Sum_probs=134.7
Q ss_pred hcccccCCCCCCCcEEEEccCCCCccchhHHHHHHHHHHHHHHHHhhcchhhhhhhCCccccEEEEEeCCCCCcccccch
Q 025326 88 QLVGVSGYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQI 167 (254)
Q Consensus 88 ~~~~~~g~D~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~l~~~~~~~~~~~~~~~~IiD~~g~~~~~~~~~ 167 (254)
.+.++ |.|++||||++++++.++++..+.+++++++++.+|...+. .....+..|+++|+|++|+++++++ .
T Consensus 9 ~~~~~-g~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~------~~~~~~~~~~~~i~D~~~~~~~~~~-~ 80 (158)
T smart00516 9 IPGGR-GYDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYVLEKILQR------EKKTGGIEGFTVIFDLKGLSMSNPD-L 80 (158)
T ss_pred cCCCC-CCCCCcCEEEEEeccccccCcCCHHHHHHHHHHHHHHHHHH------HhcCCCeeeEEEEEECCCCCccccc-H
Confidence 34444 89999999999999998888889999999999999976541 2245577899999999999999965 6
Q ss_pred HHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHHhcccCChhhhcceEEecCCCHhHHhhhCCCCCcccccCCCcc
Q 025326 168 KLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGRDELLKVRQLFQLTFLSAHSCN 245 (254)
Q Consensus 168 ~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~vk~~l~~~t~~Ki~~~~~~~~~~L~~~i~~~~LP~~~GG~~~ 245 (254)
+.++.++++++.+||++++++||+|+|++++.+|+++++|+++++++||+++++++.+.|.+++|+++||.+|||++.
T Consensus 81 ~~lk~~~~~~~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~L~~~i~~~~lP~~~GG~~~ 158 (158)
T smart00516 81 SVLRKILKILQDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGNDSKEELLEYIDPEQLPEELGGTLD 158 (158)
T ss_pred HHHHHHHHHHHHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCCCHHHHHhhCCHhhCcHhhCCCCC
Confidence 889999999999999999999999999999999999999999999999999987678999999999999999999974
No 5
>cd00170 SEC14 Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.95 E-value=1.9e-27 Score=182.47 Aligned_cols=145 Identities=30% Similarity=0.443 Sum_probs=123.9
Q ss_pred ccccCCCCCCCcEEEEccCCCCccc-hhHHHHHHHHHHHHHHHHhhcchhhhhhhCCccccEEEEEeCCCCCccccc-ch
Q 025326 90 VGVSGYSKEGLPVIAVGVGLSTHDK-ASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALN-QI 167 (254)
Q Consensus 90 ~~~~g~D~~Grpv~~~~~~~~~~~~-~~~~~~~~~~~~~~E~~~~~~l~~~~~~~~~~~~~~~~IiD~~g~~~~~~~-~~ 167 (254)
.+.+|.|++||||++++++..++.. .+.++++++.++.+|...+. .....+|+++|+|++|++++++. ..
T Consensus 11 ~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~--------~~~~~~~~~~i~D~~~~~~~~~~~~~ 82 (157)
T cd00170 11 GYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQE--------DDEQVEGFVVIIDLKGLSLSHLLPDP 82 (157)
T ss_pred cccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhh--------hhhcccceEEEEECCCCChhccchhH
Confidence 4455679999999999999644443 34478888989888875431 11223699999999999999884 46
Q ss_pred HHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHHhcccCChhhhcceEEecCCCHhHHhhhCCCCCcccccCCC
Q 025326 168 KLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGRDELLKVRQLFQLTFLSAHS 243 (254)
Q Consensus 168 ~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~vk~~l~~~t~~Ki~~~~~~~~~~L~~~i~~~~LP~~~GG~ 243 (254)
+.++.++.+++++||++++++|++|+|++++.+|+++++|+++++++||++++++ .++|.+++|+++||.+|||+
T Consensus 83 ~~~k~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~-~~~L~~~i~~~~Lp~~~GG~ 157 (157)
T cd00170 83 SLLKKILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSD-KEELLKYIDKEQLPEEYGGT 157 (157)
T ss_pred HHHHHHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCC-HHHHHhhCChhhCcHhhCCC
Confidence 7899999999999999999999999999999999999999999999999998854 89999999999999999996
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.67 E-value=5.6e-17 Score=123.82 Aligned_cols=141 Identities=15% Similarity=0.163 Sum_probs=95.2
Q ss_pred ccccCCCCCCCcEEEEccCCCCccchhHHHHHHHHHHHHHHHHhhcchhhhhhhCCccccEEEEEeCCCCCcccccchHH
Q 025326 90 VGVSGYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQIKL 169 (254)
Q Consensus 90 ~~~~g~D~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~l~~~~~~~~~~~~~~~~IiD~~g~~~~~~~~~~~ 169 (254)
.+..|+|++||||+++..... +...+.+.++.+.+..++ +. -...++++|+|++|.+..+.+....
T Consensus 4 ~~~gG~d~~g~pV~~~~~~~~-~~~~~~~~ll~yl~~~l~-------~~------~~~~~f~vVid~~~~~~~~~~~~~~ 69 (149)
T PF13716_consen 4 FYPGGRDREGRPVVVFIASRL-PSSDDLERLLLYLLSTLS-------EE------VVDKPFSVVIDHTGFSRSSEPSLSW 69 (149)
T ss_dssp -EEEEEBTTS-EEEEEEGGG--C-TTHHHHHHHHHHHHH--------TT------TTTS-EEEEEE-TT--GGG---HHH
T ss_pred EEecccCCCcCEEEEEECCcC-cchhhHHHHHHHHHHhhh-------HH------hcCCCEEEEEEcCCCccccCCchHH
Confidence 356799999999999997766 444455555555543321 11 1234699999999999877666788
Q ss_pred HHHHHHhhhhcCccccceEEEEcCCcchHHHH-HHhcccCChhh-hcceEEecCCCHhHHhhhCCCCCcccccCCCccc
Q 025326 170 MTVITTIDDLNYPEKTETYYIVNAPYIFSACW-KVVKPLLQERT-RRKMQVLQGNGRDELLKVRQLFQLTFLSAHSCNR 246 (254)
Q Consensus 170 ~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~-~~vk~~l~~~t-~~Ki~~~~~~~~~~L~~~i~~~~LP~~~GG~~~~ 246 (254)
++.+...+...|+..++++||+|++++++..+ .+.+++.+.+. ..||..+.+ .++|.++||+++||.++||+.+-
T Consensus 70 l~~~~~~l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~s--l~~L~~~i~~~qL~~~lp~~~~~ 146 (149)
T PF13716_consen 70 LKQLYKLLPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSS--LSELSKHIDPSQLPESLPGVLQY 146 (149)
T ss_dssp HHHTTTSS-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESS--TCGGGGTSGGGG------HHH--
T ss_pred HHHHHHHHHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECC--HHHHHhhCCHHHhcccCCCEEec
Confidence 99999999999999999999999999999999 66677888888 999998874 89999999999999999987653
No 7
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=99.01 E-value=8.5e-10 Score=69.21 Aligned_cols=54 Identities=30% Similarity=0.564 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHhhhHHHHHHh-hhhcCCCChHHHHHHHhhcCCCHHHHHHHHHHH
Q 025326 4 QEEIKQFQTLMEDLDDSLKETF-KNVHQGNPTDTLVRFLKARDWNVSKAHKMLVDC 58 (254)
Q Consensus 4 ~~~~~~lr~~~~~~~~~l~~~~-~~~~~~~~d~~llRfL~a~~~dv~ka~~~l~~~ 58 (254)
++++++|++.+++..... ..+ ...+...+|.+|+|||||++|||++|.++|.++
T Consensus 1 k~~l~~l~~~l~~~~~~~-~~~~~~~~~~~~d~~llRFLRARkf~v~~A~~mL~~t 55 (55)
T PF03765_consen 1 KQKLKQLREHLSELDEKA-PGLWDDEKEDHDDNFLLRFLRARKFDVEKAFKMLKKT 55 (55)
T ss_dssp HHHHHHHHHHHHH--GGG-THHHTTHTSS-SHHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhccch-hcccccccCCCCHHHHHHHHHHccCCHHHHHHHHHhC
Confidence 578899999888763222 111 234567789999999999999999999999875
No 8
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=98.43 E-value=1.3e-06 Score=74.79 Aligned_cols=126 Identities=17% Similarity=0.211 Sum_probs=93.7
Q ss_pred CCCCCCcEEEEccCCCCcc-chhHHHHHHHHHHHHHHHHhhcchhhhhhhCCccccEEEEEeCCCCCcccccchHHHHHH
Q 025326 95 YSKEGLPVIAVGVGLSTHD-KASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQIKLMTVI 173 (254)
Q Consensus 95 ~D~~Grpv~~~~~~~~~~~-~~~~~~~~~~~~~~~E~~~~~~l~~~~~~~~~~~~~~~~IiD~~g~~~~~~~~~~~~k~~ 173 (254)
.|++||+++++-..++-.. +.+--.++.+.++..++..+ +-.+.+.=-.|+...+.+.+.++...
T Consensus 89 ~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~~id~~Ve--------------~DYt~vYfh~gl~s~nkp~l~~l~~a 154 (467)
T KOG4406|consen 89 KDKQGRKIIVVYACRLPSSSELDDIRLISYLVYTIDKYVE--------------NDYTLVYFHHGLPSDNKPYLQLLFDA 154 (467)
T ss_pred ccccCCeeEEEEEecCCchhhhhhHHHHHHHHHHHHHHHh--------------ccceeeehhcCCcccccchHHHHHHH
Confidence 5999999999888775332 22222367777766665321 12566666677777777666666555
Q ss_pred HHhhhhcCccccceEEEEcCCcchHHHHHHhcccCChhhhcceEEecCCCHhHHhhhCCCCCc
Q 025326 174 TTIDDLNYPEKTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGRDELLKVRQLFQL 236 (254)
Q Consensus 174 ~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~vk~~l~~~t~~Ki~~~~~~~~~~L~~~i~~~~L 236 (254)
..-+..+|---++.+|||.+.|+.+++|+++||+++.+..+||+-++ ..++|.+++.-+.|
T Consensus 155 Yke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n--~lseL~~~l~l~rL 215 (467)
T KOG4406|consen 155 YKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFN--SLSELFEALKLNRL 215 (467)
T ss_pred HHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEee--hHHHHHHhhhhhhh
Confidence 55556678889999999999999999999999999999999999877 48999988765443
No 9
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=93.88 E-value=0.26 Score=28.72 Aligned_cols=24 Identities=21% Similarity=0.566 Sum_probs=20.3
Q ss_pred CChHHHHHHHhhcCCCHHHHHHHH
Q 025326 32 NPTDTLVRFLKARDWNVSKAHKML 55 (254)
Q Consensus 32 ~~d~~llRfL~a~~~dv~ka~~~l 55 (254)
.++.....||..++||++.|+..+
T Consensus 13 ~~~~~A~~~L~~~~wdle~Av~~y 36 (43)
T PF14555_consen 13 ADEDVAIQYLEANNWDLEAAVNAY 36 (43)
T ss_dssp SSHHHHHHHHHHTTT-HHHHHHHH
T ss_pred cCHHHHHHHHHHcCCCHHHHHHHH
Confidence 467789999999999999998876
No 10
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=93.47 E-value=0.34 Score=27.15 Aligned_cols=25 Identities=28% Similarity=0.274 Sum_probs=20.3
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHH
Q 025326 31 GNPTDTLVRFLKARDWNVSKAHKML 55 (254)
Q Consensus 31 ~~~d~~llRfL~a~~~dv~ka~~~l 55 (254)
+++.....+-|+.+++|+++|..-|
T Consensus 13 Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 13 GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 4777788999999999999998754
No 11
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=93.30 E-value=0.31 Score=28.18 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=23.3
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHHHH
Q 025326 31 GNPTDTLVRFLKARDWNVSKAHKMLVD 57 (254)
Q Consensus 31 ~~~d~~llRfL~a~~~dv~ka~~~l~~ 57 (254)
+++...+..-|.++++|++.|+..|..
T Consensus 14 ~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 14 DLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp SS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 578889999999999999999998854
No 12
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=86.33 E-value=2.5 Score=24.40 Aligned_cols=26 Identities=19% Similarity=0.204 Sum_probs=23.3
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHHH
Q 025326 31 GNPTDTLVRFLKARDWNVSKAHKMLV 56 (254)
Q Consensus 31 ~~~d~~llRfL~a~~~dv~ka~~~l~ 56 (254)
+.++..+.+.|+++++|++.|...|.
T Consensus 15 ~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 15 NLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 57888999999999999999998875
No 13
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=77.67 E-value=11 Score=23.51 Aligned_cols=27 Identities=15% Similarity=0.249 Sum_probs=24.3
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHHHH
Q 025326 31 GNPTDTLVRFLKARDWNVSKAHKMLVD 57 (254)
Q Consensus 31 ~~~d~~llRfL~a~~~dv~ka~~~l~~ 57 (254)
.++|+.+.--|+-|+.|...|+++|..
T Consensus 18 ~hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 18 CHSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 468999999999999999999999854
No 14
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=74.34 E-value=1.1 Score=30.03 Aligned_cols=26 Identities=23% Similarity=0.276 Sum_probs=21.4
Q ss_pred ChHHHHHHHhhcCCCHHHHHHHHHHH
Q 025326 33 PTDTLVRFLKARDWNVSKAHKMLVDC 58 (254)
Q Consensus 33 ~d~~llRfL~a~~~dv~ka~~~l~~~ 58 (254)
++..|..-|..++|||+||+..|.+.
T Consensus 45 ~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 45 PEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp -CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred CHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 78899999999999999999988653
No 15
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=73.28 E-value=6.9 Score=21.50 Aligned_cols=25 Identities=28% Similarity=0.410 Sum_probs=21.9
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHH
Q 025326 31 GNPTDTLVRFLKARDWNVSKAHKML 55 (254)
Q Consensus 31 ~~~d~~llRfL~a~~~dv~ka~~~l 55 (254)
+++.....+-|+.+++|+++|..-|
T Consensus 12 Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 12 GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 6888899999999999999997654
No 16
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=73.01 E-value=7.1 Score=21.57 Aligned_cols=25 Identities=28% Similarity=0.344 Sum_probs=22.3
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHH
Q 025326 31 GNPTDTLVRFLKARDWNVSKAHKML 55 (254)
Q Consensus 31 ~~~d~~llRfL~a~~~dv~ka~~~l 55 (254)
+++.....+-|+.+++|+++|...|
T Consensus 12 Gf~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 12 GFSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 6888899999999999999998765
No 17
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=69.47 E-value=16 Score=29.63 Aligned_cols=107 Identities=14% Similarity=0.217 Sum_probs=64.3
Q ss_pred HHHHHHHHHHhhcchhhhhhhCCccccEEEEEeCCCC-C-cccccchHHHHHHHHhhhhcCccccceEEEEcCCc-----
Q 025326 123 SHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGL-K-LSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPY----- 195 (254)
Q Consensus 123 ~~~~~~E~~~~~~l~~~~~~~~~~~~~~~~IiD~~g~-~-~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~----- 195 (254)
..++++||.... ++ +.....+..++--+|+||-|- . ..| +.+++.++.-++. .-.++..+|++..++
T Consensus 74 gLv~cmEyl~~N-ld-wL~~~~Gd~eddylifDcPGQIELytH---~pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~ 147 (273)
T KOG1534|consen 74 GLVYCMEYLLEN-LD-WLEEEIGDVEDDYLIFDCPGQIELYTH---LPVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDST 147 (273)
T ss_pred cchhHHHHHHHH-HH-HHHhhccCccCCEEEEeCCCeeEEeec---ChhHHHHHHHHhc-ccCceeEEEEeccchhhhHH
Confidence 347778876542 22 222233456778999999872 2 244 4467777777765 345667777666655
Q ss_pred -chHHHHHHhcccCChh-----hhcceEEecCCCHhHHhhhCCCCC
Q 025326 196 -IFSACWKVVKPLLQER-----TRRKMQVLQGNGRDELLKVRQLFQ 235 (254)
Q Consensus 196 -~~~~~~~~vk~~l~~~-----t~~Ki~~~~~~~~~~L~~~i~~~~ 235 (254)
+++.+++.++.++.-+ ...|+-++++.++++|.++.+++.
T Consensus 148 KfiSG~lsAlsAMi~lE~P~INvlsKMDLlk~~~k~~l~~Fl~~d~ 193 (273)
T KOG1534|consen 148 KFISGCLSALSAMISLEVPHINVLSKMDLLKDKNKKELERFLNPDE 193 (273)
T ss_pred HHHHHHHHHHHHHHHhcCcchhhhhHHHHhhhhhHHHHHHhcCCch
Confidence 4555555555443322 455666666556788888887653
No 18
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=56.61 E-value=30 Score=29.37 Aligned_cols=40 Identities=15% Similarity=0.046 Sum_probs=29.8
Q ss_pred chHHHHHHHHHHHHhhhHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHH
Q 025326 2 AHQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVD 57 (254)
Q Consensus 2 ~~~~~~~~lr~~~~~~~~~l~~~~~~~~~~~~d~~llRfL~a~~~dv~ka~~~l~~ 57 (254)
++.+.|++||+....-. ...-+-|..+++|+++|..-|++
T Consensus 3 isa~~IK~LRe~Tgagm----------------~dCKkAL~e~~gDiekAi~~LRk 42 (290)
T TIGR00116 3 ITAQLVKELRERTGAGM----------------MDCKKALTEANGDFEKAIKNLRE 42 (290)
T ss_pred CCHHHHHHHHHHHCCCH----------------HHHHHHHHHcCCCHHHHHHHHHH
Confidence 77888999998766433 33455677888999999887765
No 19
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=53.73 E-value=17 Score=25.12 Aligned_cols=43 Identities=26% Similarity=0.358 Sum_probs=26.3
Q ss_pred chHHHHHHHHHHHHhhhHHHHHHh--hhhcCCCChHHHHHHHhhc
Q 025326 2 AHQEEIKQFQTLMEDLDDSLKETF--KNVHQGNPTDTLVRFLKAR 44 (254)
Q Consensus 2 ~~~~~~~~lr~~~~~~~~~l~~~~--~~~~~~~~d~~llRfL~a~ 44 (254)
.|++++.++.++++.....|-.|+ ...+....+.-+++-+++.
T Consensus 44 lsd~el~~f~~LLe~~D~dL~~Wi~g~~~~~~~~~~~mv~~I~~~ 88 (94)
T COG2938 44 LSDEELDEFERLLECEDNDLFNWIMGHGEPPDAELTPMVRKIQAR 88 (94)
T ss_pred CCHHHHHHHHHHHcCCcHHHHHHHhCCCCCCcHHHHHHHHHHHHH
Confidence 367788888888887777777776 2233344455555555443
No 20
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=52.79 E-value=29 Score=19.70 Aligned_cols=24 Identities=17% Similarity=0.151 Sum_probs=19.9
Q ss_pred CChHHHHHHHhhcCCCHHHHHHHH
Q 025326 32 NPTDTLVRFLKARDWNVSKAHKML 55 (254)
Q Consensus 32 ~~d~~llRfL~a~~~dv~ka~~~l 55 (254)
.....|..-|++|++||-+|.+.+
T Consensus 15 ~kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 15 QKRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred CChHHHHHHHHHcCCcHHHHHHHh
Confidence 445678889999999999998764
No 21
>PRK09377 tsf elongation factor Ts; Provisional
Probab=50.32 E-value=42 Score=28.46 Aligned_cols=40 Identities=15% Similarity=0.072 Sum_probs=30.3
Q ss_pred chHHHHHHHHHHHHhhhHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHH
Q 025326 2 AHQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVD 57 (254)
Q Consensus 2 ~~~~~~~~lr~~~~~~~~~l~~~~~~~~~~~~d~~llRfL~a~~~dv~ka~~~l~~ 57 (254)
++.+.|++||+....- =...-+-|..+++|+++|.+-|++
T Consensus 4 is~~~IK~LR~~Tgag----------------m~dCKkAL~e~~gD~ekAi~~Lrk 43 (290)
T PRK09377 4 ITAALVKELRERTGAG----------------MMDCKKALTEADGDIEKAIEWLRK 43 (290)
T ss_pred cCHHHHHHHHHHHCCC----------------HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 6788888888876643 234556677889999999888865
No 22
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=48.76 E-value=52 Score=26.19 Aligned_cols=40 Identities=13% Similarity=0.057 Sum_probs=29.6
Q ss_pred chHHHHHHHHHHHHhhhHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHH
Q 025326 2 AHQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVD 57 (254)
Q Consensus 2 ~~~~~~~~lr~~~~~~~~~l~~~~~~~~~~~~d~~llRfL~a~~~dv~ka~~~l~~ 57 (254)
++.+.+++||+....-. ...-+-|..+++|+++|..-|++
T Consensus 3 i~a~~ik~LR~~tga~~----------------~~ck~AL~~~~gd~~~A~~~lr~ 42 (198)
T PRK12332 3 ITAKLVKELREKTGAGM----------------MDCKKALEEANGDMEKAIEWLRE 42 (198)
T ss_pred CCHHHHHHHHHHHCCCH----------------HHHHHHHHHcCCCHHHHHHHHHH
Confidence 56788888888766433 34555677888999999888876
No 23
>PF04378 RsmJ: Ribosomal RNA small subunit methyltransferase D, RsmJ; InterPro: IPR007473 This is a bacterial protein of unknown function, possibly secreted.; PDB: 2OO3_A.
Probab=47.35 E-value=9.9 Score=31.34 Aligned_cols=30 Identities=20% Similarity=0.367 Sum_probs=21.5
Q ss_pred cceEEEEcCCcchHHHHHHhcccCChhhhc
Q 025326 185 TETYYIVNAPYIFSACWKVVKPLLQERTRR 214 (254)
Q Consensus 185 l~~i~vvN~p~~~~~~~~~vk~~l~~~t~~ 214 (254)
=..++|||+||.+.-..+-+-|+|.+....
T Consensus 205 GSGm~iiNPPw~l~~~l~~~l~~L~~~L~~ 234 (245)
T PF04378_consen 205 GSGMLIINPPWTLDEELEEILPWLAETLAQ 234 (245)
T ss_dssp EEEEEEES--TTHHHHHHHHHHHHHHHSST
T ss_pred cceEEEEcCCccHHHHHHHHHHHHHHHhCc
Confidence 357999999999998888777777665544
No 24
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=46.78 E-value=13 Score=30.64 Aligned_cols=27 Identities=15% Similarity=0.330 Sum_probs=22.4
Q ss_pred ceEEEEcCCcchHHHHHHhcccCChhh
Q 025326 186 ETYYIVNAPYIFSACWKVVKPLLQERT 212 (254)
Q Consensus 186 ~~i~vvN~p~~~~~~~~~vk~~l~~~t 212 (254)
+.++|||+||.+.--...+-|+|....
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~L 263 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTLL 263 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHHh
Confidence 579999999999988888888776544
No 25
>PRK10878 hypothetical protein; Provisional
Probab=46.11 E-value=68 Score=20.96 Aligned_cols=27 Identities=11% Similarity=0.072 Sum_probs=15.0
Q ss_pred CChHHHHHHHhhcCCCHHHHHHHHHHH
Q 025326 32 NPTDTLVRFLKARDWNVSKAHKMLVDC 58 (254)
Q Consensus 32 ~~d~~llRfL~a~~~dv~ka~~~l~~~ 58 (254)
++|..|+.|+.++.--.+...+.+...
T Consensus 33 ~~D~dL~~W~~g~~~p~d~~l~~iV~~ 59 (72)
T PRK10878 33 CDDPDLFNWLMNHGKPADAELERMVRL 59 (72)
T ss_pred CCCHHHHHHHhCCCCCCCHHHHHHHHH
Confidence 566667777776654444444444443
No 26
>TIGR02886 spore_II_AA anti-sigma F factor antagonist. The anti-sigma F factor antagonist, also called stage II sporulation protein AA, is a protein universal among endospore-forming bacteria, all of which belong to the Firmcutes
Probab=44.14 E-value=88 Score=21.45 Aligned_cols=51 Identities=4% Similarity=0.042 Sum_probs=34.7
Q ss_pred EEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHHh
Q 025326 150 SLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVV 204 (254)
Q Consensus 150 ~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~v 204 (254)
-.+|+|+++++.-....+..+..+.+-++ ..=.+++++|++.-+.-++...
T Consensus 40 ~~vilDls~v~~iDssgi~~L~~~~~~~~----~~g~~l~l~~~~~~v~~~l~~~ 90 (106)
T TIGR02886 40 KHLILNLKNVTFMDSSGLGVILGRYKKIK----NEGGEVIVCNVSPAVKRLFELS 90 (106)
T ss_pred CEEEEECCCCcEecchHHHHHHHHHHHHH----HcCCEEEEEeCCHHHHHHHHHh
Confidence 48999999998876654444444444333 3447899999987776666544
No 27
>PF04838 Baculo_LEF5: Baculoviridae late expression factor 5 ; InterPro: IPR006923 This is a family of Baculoviridae late expression factor 5, required for late and very late gene expression.; GO: 0006355 regulation of transcription, DNA-dependent
Probab=44.11 E-value=20 Score=26.97 Aligned_cols=48 Identities=19% Similarity=0.441 Sum_probs=40.2
Q ss_pred HHHHHHhhhhcCccccc--eEEEEcCCcchHHHHHHhcccCCh--hhhcceEE
Q 025326 170 MTVITTIDDLNYPEKTE--TYYIVNAPYIFSACWKVVKPLLQE--RTRRKMQV 218 (254)
Q Consensus 170 ~k~~~~~~~~~yP~rl~--~i~vvN~p~~~~~~~~~vk~~l~~--~t~~Ki~~ 218 (254)
-+.++..+..+||..++ ..-+.|.+=.|.++|+-+ |-++. +-|+.|++
T Consensus 17 y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYv-P~~s~~~kERKQIRL 68 (159)
T PF04838_consen 17 YKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYV-PSVSNVEKERKQIRL 68 (159)
T ss_pred HHHHHHHHHhhcccccccCeeecCCCchhhhhhhhcc-CCCchHhHHHHHhhh
Confidence 45678888899999998 788999999999999988 77777 66677775
No 28
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=43.07 E-value=54 Score=20.81 Aligned_cols=28 Identities=18% Similarity=0.348 Sum_probs=24.1
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHHHHH
Q 025326 31 GNPTDTLVRFLKARDWNVSKAHKMLVDC 58 (254)
Q Consensus 31 ~~~d~~llRfL~a~~~dv~ka~~~l~~~ 58 (254)
+..-.+-.++|...+||.++|.+...+-
T Consensus 24 gmn~~~s~~cLe~~~Wd~~~Al~~F~~l 51 (63)
T smart00804 24 GMNAEYSQMCLEDNNWDYERALKNFTEL 51 (63)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 5677899999999999999998887553
No 29
>CHL00098 tsf elongation factor Ts
Probab=41.75 E-value=71 Score=25.49 Aligned_cols=38 Identities=16% Similarity=0.086 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHhhhHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHH
Q 025326 4 QEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVD 57 (254)
Q Consensus 4 ~~~~~~lr~~~~~~~~~l~~~~~~~~~~~~d~~llRfL~a~~~dv~ka~~~l~~ 57 (254)
.+.|++||+....- =...-+-|..+++|+++|.+-|++
T Consensus 2 a~~ik~LR~~Tgag----------------~~dck~AL~e~~gd~~~A~~~Lr~ 39 (200)
T CHL00098 2 AELVKELRDKTGAG----------------MMDCKKALQEANGDFEKALESLRQ 39 (200)
T ss_pred HHHHHHHHHHHCCC----------------HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 46677777766533 234556677888999999887766
No 30
>cd06844 STAS Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation.
Probab=38.20 E-value=1.1e+02 Score=20.77 Aligned_cols=51 Identities=6% Similarity=0.091 Sum_probs=33.4
Q ss_pred EEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHHh
Q 025326 150 SLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVV 204 (254)
Q Consensus 150 ~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~v 204 (254)
-.+|+|+++++.-....+..+..+.+.++ ..=..++++|++.-..-++...
T Consensus 40 ~~vilDls~v~~iDssgl~~L~~l~~~~~----~~g~~l~l~~~~~~v~~~l~~~ 90 (100)
T cd06844 40 KTIVIDISALEFMDSSGTGVLLERSRLAE----AVGGQFVLTGISPAVRITLTES 90 (100)
T ss_pred CEEEEECCCCcEEcHHHHHHHHHHHHHHH----HcCCEEEEECCCHHHHHHHHHh
Confidence 58999999887765544444444444443 3457899999887666555443
No 31
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=37.35 E-value=69 Score=23.49 Aligned_cols=43 Identities=7% Similarity=0.156 Sum_probs=34.6
Q ss_pred eEEEEcCCcchHHHHHHh-----cccCChhhhcceEEecCCCHhHHhhhC
Q 025326 187 TYYIVNAPYIFSACWKVV-----KPLLQERTRRKMQVLQGNGRDELLKVR 231 (254)
Q Consensus 187 ~i~vvN~p~~~~~~~~~v-----k~~l~~~t~~Ki~~~~~~~~~~L~~~i 231 (254)
-+.++|..-+.+.++..+ ..|+++.....++++.+ .+++.++|
T Consensus 86 Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d~--~~e~~~~i 133 (133)
T PF03641_consen 86 PIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVDD--PEEALEYI 133 (133)
T ss_dssp EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEESS--HHHHHHHH
T ss_pred CEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeCC--HHHHHhhC
Confidence 699999887778788766 56999999999998774 77777653
No 32
>PF01740 STAS: STAS domain; InterPro: IPR002645 The STAS (Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. The establishment of differential gene expression in sporulating Bacillus subtilis involves four protein components one of which is SpoIIAA (P10727 from SWISSPROT). The four components regulate the sporulation sigma factor F. Early in sporulation, SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase SpoIIAB (P10728 from SWISSPROT). The site at which this protein is a conserved serine. SpoIIAB is an anti-sigma factor that in its free form inhibits F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases Sigma F activity []. The STAS domain is found in the anti-sigma factor antagonist SpoIIAA.; PDB: 3T6O_B 3LKL_B 1H4Z_A 1H4Y_B 1H4X_B 3NY7_A 3OIZ_A 1T6R_A 1VC1_B 1SBO_A ....
Probab=36.50 E-value=47 Score=23.31 Aligned_cols=50 Identities=14% Similarity=0.090 Sum_probs=33.5
Q ss_pred EEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHH
Q 025326 150 SLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKV 203 (254)
Q Consensus 150 ~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~ 203 (254)
-.+|+|+++++.-....+..+..+.+.++ .+=..++++|++.-....+..
T Consensus 49 ~~vIlD~s~v~~iDssgi~~L~~~~~~~~----~~g~~~~l~~~~~~v~~~l~~ 98 (117)
T PF01740_consen 49 KNVILDMSGVSFIDSSGIQALVDIIKELR----RRGVQLVLVGLNPDVRRILER 98 (117)
T ss_dssp SEEEEEETTESEESHHHHHHHHHHHHHHH----HTTCEEEEESHHHHHHHHHHH
T ss_pred eEEEEEEEeCCcCCHHHHHHHHHHHHHHH----HCCCEEEEEECCHHHHHHHHH
Confidence 58999999887655444444555544444 466889999998766655443
No 33
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=36.15 E-value=58 Score=18.44 Aligned_cols=22 Identities=32% Similarity=0.333 Sum_probs=18.4
Q ss_pred hHHHHHHHhhcCCCHHHHHHHH
Q 025326 34 TDTLVRFLKARDWNVSKAHKML 55 (254)
Q Consensus 34 d~~llRfL~a~~~dv~ka~~~l 55 (254)
..++..-|..++||+.+|.+.|
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHH
Confidence 4578889999999999999887
No 34
>PHA02450 hypothetical protein
Probab=35.84 E-value=15 Score=21.51 Aligned_cols=12 Identities=25% Similarity=0.357 Sum_probs=9.8
Q ss_pred ccCCCccccchh
Q 025326 239 LSAHSCNRLTIY 250 (254)
Q Consensus 239 ~~GG~~~~~~~~ 250 (254)
.|||+|.|-..|
T Consensus 12 ryggdc~cg~iy 23 (53)
T PHA02450 12 RYGGDCTCGPIY 23 (53)
T ss_pred eeCCccccccee
Confidence 599999997665
No 35
>PF03937 Sdh5: Flavinator of succinate dehydrogenase; InterPro: IPR005631 This entry represents a group of uncharacterised small proteins found in both eukaryotes and prokaryotes, including NMA1147 from Neisseria meningitidis [] and YgfY from Escherichia coli []. YgfY may be involved in transcriptional regulation. The structure of these proteins consists of a complex bundle of five alpha-helices, which is composed of an up-down 3-helix bundle plus an orthogonal 2-helix bundle. ; PDB: 2LM4_A 1PUZ_A 2JR5_A 1X6I_A 1X6J_A.
Probab=34.83 E-value=61 Score=21.17 Aligned_cols=23 Identities=26% Similarity=0.445 Sum_probs=11.7
Q ss_pred hHHHHHHHHHHHHhhhHHHHHHh
Q 025326 3 HQEEIKQFQTLMEDLDDSLKETF 25 (254)
Q Consensus 3 ~~~~~~~lr~~~~~~~~~l~~~~ 25 (254)
++++++++..+++.....|-.|+
T Consensus 33 ~~~el~~fe~lL~~~D~dL~~wl 55 (74)
T PF03937_consen 33 SEEELDAFERLLDLEDPDLYDWL 55 (74)
T ss_dssp -HHHHHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHcCCCHHHHHHH
Confidence 44556666666665554444444
No 36
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=33.98 E-value=34 Score=20.62 Aligned_cols=26 Identities=15% Similarity=0.329 Sum_probs=20.5
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHHH
Q 025326 31 GNPTDTLVRFLKARDWNVSKAHKMLV 56 (254)
Q Consensus 31 ~~~d~~llRfL~a~~~dv~ka~~~l~ 56 (254)
+.+-.+-.++|..++||.++|.+...
T Consensus 12 gmn~~~s~~CL~~n~Wd~~~A~~~F~ 37 (51)
T PF03943_consen 12 GMNLEWSQKCLEENNWDYERALQNFE 37 (51)
T ss_dssp SS-CCHHHHHHHHTTT-CCHHHHHHH
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45667899999999999999988764
No 37
>TIGR00377 ant_ant_sig anti-anti-sigma factor. This superfamily includes small (105-125 residue) proteins related to SpoIIAA of Bacillus subtilis, an anti-anti-sigma factor. SpoIIAA can bind to and inhibit the anti-sigma F factor SpoIIAB. Also, it can be phosphorylated by SpoIIAB on a Ser residue at position 59 of the seed alignment. A similar arrangement is inferred for RsbV, an anti-anti-sigma factor for sigma B. This Ser is fairly well conserved within a motif resembling MXS[STA]G[VIL]X[VIL][VILF] among homologous known or predicted anti-anti-sigma factors. Regions similar to SpoIIAA and apparently homologous, but differing considerably near the phosphorlated Ser of SpoIIAA, appear in a single copy in several longer proteins.
Probab=33.54 E-value=1.6e+02 Score=20.10 Aligned_cols=52 Identities=10% Similarity=0.040 Sum_probs=34.5
Q ss_pred cEEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHHh
Q 025326 149 TSLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVV 204 (254)
Q Consensus 149 ~~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~v 204 (254)
.-.+++|+++++.-....+..+..+...++ +.=..+.+++++.-+.-++...
T Consensus 43 ~~~vvidls~v~~iDssgl~~L~~~~~~~~----~~~~~~~l~~~~~~~~~~l~~~ 94 (108)
T TIGR00377 43 PRPIVLDLEDLEFMDSSGLGVLLGRYKQVR----RVGGQLVLVSVSPRVARLLDIT 94 (108)
T ss_pred CCeEEEECCCCeEEccccHHHHHHHHHHHH----hcCCEEEEEeCCHHHHHHHHHh
Confidence 347999999888766554555555554444 2346799999887666666544
No 38
>COG2994 HlyC ACP:hemolysin acyltransferase (hemolysin-activating protein) [Posttranslational modification, protein turnover, chaperones]
Probab=32.75 E-value=56 Score=24.38 Aligned_cols=71 Identities=8% Similarity=0.175 Sum_probs=37.8
Q ss_pred CCCCCCCcEEEEccCCCCccchhHHHHHHHHHHHHHHHHhhcchhhhhhhCCccccEEEEEeCCCCCcccccchHHHHHH
Q 025326 94 GYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQIKLMTVI 173 (254)
Q Consensus 94 g~D~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~l~~~~~~~~~~~~~~~~IiD~~g~~~~~~~~~~~~k~~ 173 (254)
-+|++|+||.++.-...+.+ ..++++..-. .....+...+.-++|+|.- .. +.-.+.+
T Consensus 57 y~de~g~Piaf~~WA~vde~--~e~~lL~~~~-------------~l~p~dW~SG~~iwii~~i----AP---fGh~r~~ 114 (148)
T COG2994 57 YFDEHGRPIAFCTWAFVDEQ--AEEELLENDR-------------NLSPEDWASGNNIWIIDWI----AP---FGHSRQM 114 (148)
T ss_pred EEcCCCCeeEEEEEeecCHH--HHHHHHhCCC-------------CCChhhccCCCeeEEEEEE----cc---CCchHHH
Confidence 36899999999887664432 2222221100 1111233445668888862 11 2223333
Q ss_pred H-HhhhhcCccccc
Q 025326 174 T-TIDDLNYPEKTE 186 (254)
Q Consensus 174 ~-~~~~~~yP~rl~ 186 (254)
. ++.+..||.+..
T Consensus 115 ~~dl~~~lFp~~~v 128 (148)
T COG2994 115 VKDLHRNLFPDRTV 128 (148)
T ss_pred HHHHHHHhCchhhh
Confidence 3 667788888743
No 39
>cd07041 STAS_RsbR_RsbS_like Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain of proteins related to RsbS and RsbR which are part of the "stressosome" complex that plays an important role in the regulation of the bacterial stress activated alternative sigma factor sigma-B. During stress conditions RsbS and RsbR are phosphorylated which leads to the release of RsbT, an activator of of the RsbU phosphatase, which in turn activates RsbV which leads to the release and activation of sigma factor B. RsbS is a single domain protein (STAS domain), while RsbR-like proteins have a well-conserved C-terminal STATS domain and a variable N-terminal domain. The STAS domain is also found in the C- terminal region of sulphate transporters and anti-anti-sigma factors.
Probab=32.06 E-value=1.5e+02 Score=20.34 Aligned_cols=51 Identities=6% Similarity=-0.025 Sum_probs=33.3
Q ss_pred EEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHHh
Q 025326 150 SLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVV 204 (254)
Q Consensus 150 ~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~v 204 (254)
-.+|+|+++++.-....+..+..+.+.+. .+=.++++++...-+.-++...
T Consensus 42 ~~vvlDls~v~~iDssg~~~l~~~~~~~~----~~g~~l~l~g~~~~v~~~l~~~ 92 (109)
T cd07041 42 RGVIIDLTGVPVIDSAVARHLLRLARALR----LLGARTILTGIRPEVAQTLVEL 92 (109)
T ss_pred CEEEEECCCCchhcHHHHHHHHHHHHHHH----HcCCeEEEEeCCHHHHHHHHHh
Confidence 48999999888766544444444444333 3447899999876666555444
No 40
>cd07043 STAS_anti-anti-sigma_factors Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation. Anti-anti-sigma factors play an important role in the regulation of several sigma factors and their corresponding anti-sigma factors. Upon dephosphorylation they bind the anti-sigma factor and induce the release of the sigma factor from the anti-sigma factor. In a feedback mechanism the anti-anti-sigma factor can be inactivated via phosphorylation by the anti-sigma factor. Well studied examples from Bacillus subtilis are SpoIIAA (regulating sigmaF and sigmaC which play an important role in sporulation) and RsbV (regulating sigmaB involved in the general stress response). The STAS domain is also found in the C- terminal region of sulphate transporters and stressosomes.
Probab=31.95 E-value=1.5e+02 Score=19.52 Aligned_cols=51 Identities=12% Similarity=0.125 Sum_probs=33.0
Q ss_pred EEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHHh
Q 025326 150 SLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVV 204 (254)
Q Consensus 150 ~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~v 204 (254)
-.+++|+++++.-....+..+..+.+.+. .+=..+.+.+++.-..-++..+
T Consensus 39 ~~viid~~~v~~iDs~g~~~L~~l~~~~~----~~g~~v~i~~~~~~~~~~l~~~ 89 (99)
T cd07043 39 RRLVLDLSGVTFIDSSGLGVLLGAYKRAR----AAGGRLVLVNVSPAVRRVLELT 89 (99)
T ss_pred CEEEEECCCCCEEcchhHHHHHHHHHHHH----HcCCeEEEEcCCHHHHHHHHHh
Confidence 47889999877665443444444443333 3347799999987777666655
No 41
>PF04548 AIG1: AIG1 family; InterPro: IPR006703 This entry represents a domain found in Arabidopsis protein AIG1 which appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 (avrRpt2-induced gene) exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2 []. The domain is also apparently found in a number of mammalian proteins, for example the rat immune-associated nucleotide 4 protein. ; GO: 0005525 GTP binding; PDB: 3LXX_A 3BB4_A 3DEF_A 3BB3_A 2J3E_A 3V70_B 3BB1_A 1H65_B 2XTP_A 3P1J_C ....
Probab=31.84 E-value=1.9e+02 Score=22.94 Aligned_cols=71 Identities=14% Similarity=0.170 Sum_probs=46.9
Q ss_pred cEEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCCcch---HHHHHHhcccCChhhhcceEEe
Q 025326 149 TSLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIF---SACWKVVKPLLQERTRRKMQVL 219 (254)
Q Consensus 149 ~~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~---~~~~~~vk~~l~~~t~~Ki~~~ 219 (254)
.-+.|+|.-|+.=.....-...+.+...+..+.|..=.-++|++..++- ..++..+...+.++..+.+.++
T Consensus 49 ~~v~VIDTPGl~d~~~~~~~~~~~i~~~l~~~~~g~ha~llVi~~~r~t~~~~~~l~~l~~~FG~~~~k~~ivv 122 (212)
T PF04548_consen 49 RQVTVIDTPGLFDSDGSDEEIIREIKRCLSLCSPGPHAFLLVIPLGRFTEEDREVLELLQEIFGEEIWKHTIVV 122 (212)
T ss_dssp EEEEEEE--SSEETTEEHHHHHHHHHHHHHHTTT-ESEEEEEEETTB-SHHHHHHHHHHHHHHCGGGGGGEEEE
T ss_pred eEEEEEeCCCCCCCcccHHHHHHHHHHHHHhccCCCeEEEEEEecCcchHHHHHHHHHHHHHccHHHHhHhhHH
Confidence 5578999998754444333456777777777888776788899988764 4667777777787777776554
No 42
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=31.60 E-value=1.5e+02 Score=19.17 Aligned_cols=49 Identities=14% Similarity=0.043 Sum_probs=29.0
Q ss_pred EEEEEeCCCCCcccccchHHHHHHHHhhhhcCc--cccceEEEEcCCcchHHHH
Q 025326 150 SLKVLDMTGLKLSALNQIKLMTVITTIDDLNYP--EKTETYYIVNAPYIFSACW 201 (254)
Q Consensus 150 ~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP--~rl~~i~vvN~p~~~~~~~ 201 (254)
-.+++|+.|+..-.- +++-...--+...|| +.-.++.++|++.....+.
T Consensus 18 ~~V~lDF~gv~~~~s---sFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I 68 (74)
T PF14213_consen 18 EKVVLDFEGVESITS---SFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMI 68 (74)
T ss_pred CeEEEECCCcccccH---HHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHH
Confidence 348999999954321 333333333334455 4567888999886665443
No 43
>cd00392 Ribosomal_L13 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.
Probab=31.46 E-value=1.1e+02 Score=21.96 Aligned_cols=38 Identities=24% Similarity=0.238 Sum_probs=23.2
Q ss_pred EEEeCCCCCcccccchHHHHHHHHhhhh-----cCcc--ccceEEEEcCC
Q 025326 152 KVLDMTGLKLSALNQIKLMTVITTIDDL-----NYPE--KTETYYIVNAP 194 (254)
Q Consensus 152 ~IiD~~g~~~~~~~~~~~~k~~~~~~~~-----~yP~--rl~~i~vvN~p 194 (254)
+|+|++|-.+.. +...++++++. +.|. +=..|.|||+-
T Consensus 2 ~viDA~~~~lGR-----lAs~iA~~L~gKhKp~y~p~~d~Gd~VvViNa~ 46 (114)
T cd00392 2 HVIDAKGQVLGR-----LASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAE 46 (114)
T ss_pred EEEeCCCCchHH-----HHHHHHHHHcCCCCCCcCCCccCCCEEEEEecc
Confidence 578888766654 34445555543 4443 45668888873
No 44
>PF13466 STAS_2: STAS domain
Probab=30.80 E-value=1.5e+02 Score=19.02 Aligned_cols=51 Identities=10% Similarity=0.186 Sum_probs=33.6
Q ss_pred EEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHHh
Q 025326 150 SLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVV 204 (254)
Q Consensus 150 ~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~v 204 (254)
-.+++|+++++.-....+.++-...... ...=..+.+.|+|.-+..++.+.
T Consensus 27 ~~v~lDls~v~~iDsagl~lL~~~~~~~----~~~g~~~~l~~~~~~~~~ll~~~ 77 (80)
T PF13466_consen 27 RPVVLDLSGVEFIDSAGLQLLLAAARRA----RARGRQLRLTGPSPALRRLLELL 77 (80)
T ss_pred CeEEEECCCCCeecHHHHHHHHHHHHHH----HHCCCeEEEEcCCHHHHHHHHHh
Confidence 6889999988876654444333333332 24557888999998777666553
No 45
>TIGR02364 dha_pts dihydroxyacetone kinase, phosphotransfer subunit. In E. coli and many other bacteria, unlike the yeasts and a few bacteria such as Citrobacter freundii, the dihydroxyacetone kinase (also called glycerone kinase) transfers a phosphate from a phosphoprotein rather than from ATP and contains multiple subunits. This protein, which resembles proteins of PTS transport systems, is found with its gene adjacent to
Probab=30.60 E-value=1.3e+02 Score=21.92 Aligned_cols=50 Identities=18% Similarity=0.250 Sum_probs=34.3
Q ss_pred cccEEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHHhcc
Q 025326 147 IGTSLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVKP 206 (254)
Q Consensus 147 ~~~~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~vk~ 206 (254)
..+++++.|+ |-+..+.. . .+..++ ++....+..+|.|.+...+-..+..
T Consensus 59 ~dgVlvl~DL-Ggs~~n~e---~---a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~ 108 (125)
T TIGR02364 59 ADGVLIFYDL-GSAVMNAE---M---AVELLE---DEDRDKVHLVDAPLVEGAFAAAVEA 108 (125)
T ss_pred CCCEEEEEcC-CCcHhHHH---H---HHHHhc---cccccEEEEechhHHHHHHHHHHHH
Confidence 3689999999 66654321 1 122222 3556889999999999988877754
No 46
>cd07042 STAS_SulP_like_sulfate_transporter Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
Probab=29.45 E-value=1.6e+02 Score=19.85 Aligned_cols=50 Identities=6% Similarity=0.096 Sum_probs=30.4
Q ss_pred EEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCCcchHHHHHH
Q 025326 150 SLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKV 203 (254)
Q Consensus 150 ~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~~ 203 (254)
..+|+|+++++.-....+..+..+...+. .+=..+.+.|++.-+.-++..
T Consensus 42 ~~lilD~~~v~~iDss~~~~L~~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 91 (107)
T cd07042 42 KVVILDLSAVNFIDSTAAEALEELVKDLR----KRGVELYLAGLNPQVRELLER 91 (107)
T ss_pred eEEEEECCCCchhhHHHHHHHHHHHHHHH----HCCCEEEEecCCHHHHHHHHH
Confidence 57899999887654333333444433333 344788999998755544443
No 47
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=28.90 E-value=1.4e+02 Score=18.06 Aligned_cols=25 Identities=12% Similarity=0.004 Sum_probs=16.3
Q ss_pred HHHHHHhhcCCCHHHHHHHHHHHHH
Q 025326 36 TLVRFLKARDWNVSKAHKMLVDCLR 60 (254)
Q Consensus 36 ~llRfL~a~~~dv~ka~~~l~~~~~ 60 (254)
+.+-.+.....+.++|...+...++
T Consensus 35 ~~lg~~~~~~g~~~~A~~~~~~a~~ 59 (65)
T PF13432_consen 35 YLLGRILYQQGRYDEALAYYERALE 59 (65)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 4444555567799999888877653
No 48
>cd01886 EF-G Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group conta
Probab=28.53 E-value=2.6e+02 Score=23.28 Aligned_cols=35 Identities=3% Similarity=-0.031 Sum_probs=27.5
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhC
Q 025326 31 GNPTDTLVRFLKARDWNVSKAHKMLVDCLRWRIEN 65 (254)
Q Consensus 31 ~~~d~~llRfL~a~~~dv~ka~~~l~~~~~wR~~~ 65 (254)
..||+.+-|||-.-..+.+...+.|++.+.=++-+
T Consensus 209 e~dd~L~e~yl~~~~~~~~el~~~l~~~~~~~~~~ 243 (270)
T cd01886 209 EFDDELMEKYLEGEEITEEEIKAAIRKGTIANKIV 243 (270)
T ss_pred cCCHHHHHHHhCCCCCCHHHHHHHHHHHHHcCcEE
Confidence 47999999999999888888888887766544433
No 49
>KOG1838 consensus Alpha/beta hydrolase [General function prediction only]
Probab=28.41 E-value=4.4e+02 Score=23.67 Aligned_cols=85 Identities=20% Similarity=0.246 Sum_probs=54.9
Q ss_pred CCCCcEEEEccCCCCccchhHHHHHHHHHHHHHHHHhhcchhhhhhhCCccccEEEEEeCCCCCcccccc--------hH
Q 025326 97 KEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQ--------IK 168 (254)
Q Consensus 97 ~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~l~~~~~~~~~~~~~~~~IiD~~g~~~~~~~~--------~~ 168 (254)
.+..|++++-+|.- ..+.+.++++.+.. +.+. .--++|++-+|++-+.+.. -.
T Consensus 122 ~~~~P~vvilpGlt---g~S~~~YVr~lv~~-----------a~~~-----G~r~VVfN~RG~~g~~LtTpr~f~ag~t~ 182 (409)
T KOG1838|consen 122 DGTDPIVVILPGLT---GGSHESYVRHLVHE-----------AQRK-----GYRVVVFNHRGLGGSKLTTPRLFTAGWTE 182 (409)
T ss_pred CCCCcEEEEecCCC---CCChhHHHHHHHHH-----------HHhC-----CcEEEEECCCCCCCCccCCCceeecCCHH
Confidence 35669999998863 22334566665521 1111 2458899999977666531 24
Q ss_pred HHHHHHHhhhhcCccccceEEEEcCCcchHHHHH
Q 025326 169 LMTVITTIDDLNYPEKTETYYIVNAPYIFSACWK 202 (254)
Q Consensus 169 ~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~ 202 (254)
-++.+++.+...||.+ +++.+-.+..-..+++
T Consensus 183 Dl~~~v~~i~~~~P~a--~l~avG~S~Gg~iL~n 214 (409)
T KOG1838|consen 183 DLREVVNHIKKRYPQA--PLFAVGFSMGGNILTN 214 (409)
T ss_pred HHHHHHHHHHHhCCCC--ceEEEEecchHHHHHH
Confidence 5899999999999996 6666666555555554
No 50
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=27.79 E-value=51 Score=27.19 Aligned_cols=65 Identities=8% Similarity=0.042 Sum_probs=43.9
Q ss_pred cCccccceEEEEcCCcchHHHHHHhcccCChhh--hcceEEecCC-----CHhHHhhhCCCCCccc-ccCCCccc
Q 025326 180 NYPEKTETYYIVNAPYIFSACWKVVKPLLQERT--RRKMQVLQGN-----GRDELLKVRQLFQLTF-LSAHSCNR 246 (254)
Q Consensus 180 ~yP~rl~~i~vvN~p~~~~~~~~~vk~~l~~~t--~~Ki~~~~~~-----~~~~L~~~i~~~~LP~-~~GG~~~~ 246 (254)
-|.+| ..+||||.-.....+-.. -.|+.... -.+|-|++.. ...+.++..+.-++.. .+||+.+.
T Consensus 31 If~~R-ngihIIDL~kT~~~l~~A-~~~v~~~~~~~g~ILfVgTK~~a~~~V~~~A~r~g~~yV~~RwLgG~LTN 103 (252)
T COG0052 31 IFGER-NGIHIIDLQKTLERLREA-YKFLRRIAANGGKILFVGTKKQAQEPVKEFAERTGAYYVNGRWLGGMLTN 103 (252)
T ss_pred ceeec-CCcEEEEHHHHHHHHHHH-HHHHHHHHcCCCEEEEEechHHHHHHHHHHHHHhCCceecCcccCccccC
Confidence 68899 999999986554433222 23455444 5778888864 2455666777777755 79999976
No 51
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=27.09 E-value=34 Score=29.57 Aligned_cols=22 Identities=27% Similarity=0.628 Sum_probs=19.4
Q ss_pred hHHHHHHHhhcCCCHHHHHHHH
Q 025326 34 TDTLVRFLKARDWNVSKAHKML 55 (254)
Q Consensus 34 d~~llRfL~a~~~dv~ka~~~l 55 (254)
...++|.|.+++|||++|.+-+
T Consensus 144 ENillkLlqaadydV~rAerGI 165 (408)
T COG1219 144 ENILLKLLQAADYDVERAERGI 165 (408)
T ss_pred HHHHHHHHHHcccCHHHHhCCe
Confidence 4689999999999999997664
No 52
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=24.98 E-value=1.4e+02 Score=22.57 Aligned_cols=66 Identities=8% Similarity=0.065 Sum_probs=38.1
Q ss_pred ccEEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCC---cc-----hHHHHHHhcccCC------hhhh
Q 025326 148 GTSLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAP---YI-----FSACWKVVKPLLQ------ERTR 213 (254)
Q Consensus 148 ~~~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p---~~-----~~~~~~~vk~~l~------~~t~ 213 (254)
...++|++++.+.++.-- .. ....-.+|+ ..+.. .|+- .+ -..+++.|+.+|+ ....
T Consensus 28 Gd~VVViNa~kv~~tG~K----~~--~~~~y~~~~-~~k~~--~np~~~~~~~~r~P~~il~~AV~gMLP~kn~~gr~~~ 98 (146)
T PRK06394 28 GEEVVIVNAEKAVITGNR----ER--VIEKYKQRR-ERGSH--YNPYRNGPKYPRRPDRIFKRTIRGMLPYKKPRGREAL 98 (146)
T ss_pred CCEEEEEechheEecCch----hh--heeeEeCCC-CCccc--CCCCChHHhhhcCHHHHHHHHHHhcCCCCChhHHHHH
Confidence 568899999888776521 01 112223455 22322 4421 11 3578889999999 2356
Q ss_pred cceEEecCC
Q 025326 214 RKMQVLQGN 222 (254)
Q Consensus 214 ~Ki~~~~~~ 222 (254)
+|++++.+.
T Consensus 99 ~rLkvy~G~ 107 (146)
T PRK06394 99 KRLKVYVGV 107 (146)
T ss_pred hCcEEecCC
Confidence 678877653
No 53
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=24.83 E-value=1.5e+02 Score=17.23 Aligned_cols=44 Identities=16% Similarity=0.319 Sum_probs=28.4
Q ss_pred hHHHHHHHHHHHHhhhHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHH
Q 025326 3 HQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSK 50 (254)
Q Consensus 3 ~~~~~~~lr~~~~~~~~~l~~~~~~~~~~~~d~~llRfL~a~~~dv~k 50 (254)
|.++++++-+.+.+.+ .+++.+.. --+...++.+.+..+|+...
T Consensus 2 S~~~l~~Fl~~~~~d~-~l~~~l~~---~~~~~e~~~lA~~~Gy~ft~ 45 (49)
T PF07862_consen 2 SIESLKAFLEKVKSDP-ELREQLKA---CQNPEEVVALAREAGYDFTE 45 (49)
T ss_pred CHHHHHHHHHHHhcCH-HHHHHHHh---cCCHHHHHHHHHHcCCCCCH
Confidence 5677777777776544 34443322 22667888899988888654
No 54
>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by TIGR01066.
Probab=24.30 E-value=1.1e+02 Score=22.86 Aligned_cols=68 Identities=13% Similarity=0.142 Sum_probs=36.8
Q ss_pred cccEEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccc------eEEEEcCCcchHHHHHHhcccCChh------hhc
Q 025326 147 IGTSLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTE------TYYIVNAPYIFSACWKVVKPLLQER------TRR 214 (254)
Q Consensus 147 ~~~~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~------~i~vvN~p~~~~~~~~~vk~~l~~~------t~~ 214 (254)
....++|++++.+.++.-- ...-. .....+|.... .++--+| -..++..|+.+|+.+ ..+
T Consensus 23 ~Gd~VvViNaeki~~TG~k----~~~k~-~y~~~~~~g~~~~~~~~~~~~r~P---~~il~~aVrGMLPk~~~~Gr~~~k 94 (142)
T TIGR01077 23 NGEKVVVVNAEKIVISGNF----YRNKL-KYKEFLRKRTLTNPRRGPFFPRAP---SRIFRRTVRGMLPHKTARGRAALR 94 (142)
T ss_pred cCCEEEEEechHheecCch----hhhee-EEEEECCCCCcccCCHHHhhhcCH---HHHHHHHHHHhCCCCChhHHHHHh
Confidence 4668889998887776521 00000 01112333222 2233223 256778888888875 356
Q ss_pred ceEEecCC
Q 025326 215 KMQVLQGN 222 (254)
Q Consensus 215 Ki~~~~~~ 222 (254)
|++++.+.
T Consensus 95 rLkvy~G~ 102 (142)
T TIGR01077 95 RLKVYVGI 102 (142)
T ss_pred CcEEecCC
Confidence 77877653
No 55
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=24.25 E-value=2.1e+02 Score=24.38 Aligned_cols=40 Identities=13% Similarity=0.060 Sum_probs=28.9
Q ss_pred chHHHHHHHHHHHHhhhHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHH
Q 025326 2 AHQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVD 57 (254)
Q Consensus 2 ~~~~~~~~lr~~~~~~~~~l~~~~~~~~~~~~d~~llRfL~a~~~dv~ka~~~l~~ 57 (254)
++.+.+++||+..+.-. ..+=+-|..+++|.++|.+-|++
T Consensus 4 ita~~VKeLRe~TgAGM----------------mdCKkAL~E~~Gd~EkAie~LR~ 43 (296)
T COG0264 4 ITAALVKELREKTGAGM----------------MDCKKALEEANGDIEKAIEWLRE 43 (296)
T ss_pred ccHHHHHHHHHHhCCcH----------------HHHHHHHHHcCCCHHHHHHHHHH
Confidence 57788888888776543 23455677788999999877755
No 56
>PF12452 DUF3685: Protein of unknown function (DUF3685) ; InterPro: IPR022552 This entry represents proteins annotated as Ycf55. It is found encoded in the chloroplast genomes of algae, it is also found in plants and in the cyanobacteria. The function is unknown, though there are two completely conserved residues (L and D) that may be functionally important. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis. Some members of this family are predicted to be response regulators because they contain an N-terminal CheY-like receiver domain.
Probab=23.66 E-value=3.5e+02 Score=21.50 Aligned_cols=65 Identities=12% Similarity=0.210 Sum_probs=50.2
Q ss_pred chHHHHHHHHHHHHhhhHHHHHHh-hh-hcCCCChHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhCC
Q 025326 2 AHQEEIKQFQTLMEDLDDSLKETF-KN-VHQGNPTDTLVRFLKARDWNVSKAHKMLVDCLRWRIEND 66 (254)
Q Consensus 2 ~~~~~~~~lr~~~~~~~~~l~~~~-~~-~~~~~~d~~llRfL~a~~~dv~ka~~~l~~~~~wR~~~~ 66 (254)
.++++++++.-++++..-.+.+.+ +. +..-.++..+-+.+-..++--.+..+++++.+.|+....
T Consensus 31 ~~~~a~~~~e~lLeNllI~~An~V~~~lLn~~s~~~~ik~~l~~~~llSTReLeRfRN~L~~~~r~~ 97 (193)
T PF12452_consen 31 DSPEAILRLEILLENLLIQVANGVAQPLLNNFSDWEEIKQYLYNSSLLSTRELERFRNELSWQYRWQ 97 (193)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHhcchhhhchHHHHHHHHHHHHHHHHH
Confidence 367888989899999887777776 33 233445667777777778877899999999999998863
No 57
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=23.62 E-value=2e+02 Score=22.08 Aligned_cols=59 Identities=12% Similarity=0.184 Sum_probs=41.0
Q ss_pred chHHHHHHHHHHHHhhhHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhC
Q 025326 2 AHQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVDCLRWRIEN 65 (254)
Q Consensus 2 ~~~~~~~~lr~~~~~~~~~l~~~~~~~~~~~~d~~llRfL~a~~~dv~ka~~~l~~~~~wR~~~ 65 (254)
.++++-+++|+++++.....+. ...-+-.-+..-+++.+||-.++...+.+..+-+.+.
T Consensus 57 LTd~QR~qmr~im~~~r~~~~~-----~~~~~~~~m~~Li~Ad~FDeaAvra~~~kma~~~~e~ 115 (162)
T PRK12751 57 LTEQQRQQMRDLMRQSHQSQPR-----LDLEDREAMHKLITADKFDEAAVRAQAEKMSQNQIER 115 (162)
T ss_pred CCHHHHHHHHHHHHHhhhcccc-----hhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 3678899999999887653211 0011234678899999999999988887766555543
No 58
>PF13551 HTH_29: Winged helix-turn helix
Probab=22.97 E-value=2.4e+02 Score=19.22 Aligned_cols=17 Identities=18% Similarity=0.231 Sum_probs=12.2
Q ss_pred chHHHHHHHHHHHHhhh
Q 025326 2 AHQEEIKQFQTLMEDLD 18 (254)
Q Consensus 2 ~~~~~~~~lr~~~~~~~ 18 (254)
.++++.+.+.+++.+.+
T Consensus 58 l~~~~~~~l~~~~~~~p 74 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENP 74 (112)
T ss_pred CCHHHHHHHHHHHHHCC
Confidence 35677788888777754
No 59
>KOG3923 consensus D-aspartate oxidase [Amino acid transport and metabolism]
Probab=21.77 E-value=92 Score=26.70 Aligned_cols=44 Identities=25% Similarity=0.357 Sum_probs=36.6
Q ss_pred ccEEEEEeCCCCCcccccchHHHHHHHHhhhhcCccccceEEEEcCCcchHHHHH
Q 025326 148 GTSLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWK 202 (254)
Q Consensus 148 ~~~~~IiD~~g~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~vvN~p~~~~~~~~ 202 (254)
.++-+|++|.|+.-+.+.. .+..||-| ++|.-|.+||...+++.
T Consensus 182 ~~~DVivNCtGL~a~~L~g----------Dd~~yPiR-GqVl~V~ApWvkhf~~~ 225 (342)
T KOG3923|consen 182 PEYDVIVNCTGLGAGKLAG----------DDDLYPIR-GQVLKVDAPWVKHFIYR 225 (342)
T ss_pred CCCcEEEECCccccccccC----------Ccceeecc-ceEEEeeCCceeEEEEe
Confidence 5789999999999887642 13489999 99999999999887774
No 60
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=20.50 E-value=1.8e+02 Score=22.33 Aligned_cols=28 Identities=11% Similarity=0.163 Sum_probs=16.7
Q ss_pred cCCCChHHHHHHHhhcCCCHHH-HHHHHH
Q 025326 29 HQGNPTDTLVRFLKARDWNVSK-AHKMLV 56 (254)
Q Consensus 29 ~~~~~d~~llRfL~a~~~dv~k-a~~~l~ 56 (254)
..+++|.-+..-|...+.++++ ++.+++
T Consensus 119 ~~PlSD~~i~~~L~~~gi~isRRTVaKYR 147 (160)
T PF04552_consen 119 KKPLSDQEIAELLKEEGIKISRRTVAKYR 147 (160)
T ss_dssp TS---HHHHHHHHTTTTS---HHHHHHHH
T ss_pred CCCCCHHHHHHHHHHcCCCccHHHHHHHH
Confidence 4578999999999999988774 444443
No 61
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=20.27 E-value=3e+02 Score=18.90 Aligned_cols=62 Identities=13% Similarity=0.191 Sum_probs=41.7
Q ss_pred chHHHHHHHHHHHHhhhHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhC
Q 025326 2 AHQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVDCLRWRIEN 65 (254)
Q Consensus 2 ~~~~~~~~lr~~~~~~~~~l~~~~~~~~~~~~d~~llRfL~a~~~dv~ka~~~l~~~~~wR~~~ 65 (254)
.++++.+++++++++.......--.... --...+..-+.+-++|-++..+.+.+....+.+.
T Consensus 42 Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~--~~r~~l~~ll~~~~~D~~~i~a~~~~~~~~~~~l 103 (125)
T PF13801_consen 42 LTPEQQAKLRALMDEFRQEMRALRQELR--AARQELRALLAAPPPDEAAIEALLEEIREAQAEL 103 (125)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHCCSSS-HHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 4678888888888876543332211111 1134678888899999999988888887777765
Done!